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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ), 'gf_id' => 'HOM05D001342', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001342' ), 'data_identifier' => 'HOM05D001342', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001342', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '469', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p13250' => 'bna', 'A06p37500' => 'bna', 'A06p37520' => 'bna', 'A07p13910' => 'bna', 'A07p30270' => 'bna', 'A07p37000' => 'bna', 'A08p12330' => 'bna', 'A08p28240' => 'bna', 'A08p30960' => 'bna', 'A08p30980' => 'bna', 'A09p41450' => 'bna', 'A09p60470' => 'bna', 'Aa31LG4G2700' => 'aar', 'Aa31LG7G2120' => 'aar', 'Aa31LG7G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3518' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3423' => 'aag', 'Actinidia15083' => 'ach', 'Actinidia21836' => 'ach', 'Actinidia24428' => 'ach', 'Actinidia24429' => 'ach', 'Actinidia37420' => 'ach', 'Ah.03g133130' => 'amhyb', 'Ah.08g217380' => 'amhyb', 'Ah.15g094930' => 'amhyb', 'Ah.15g094940' => 'amhyb', 'AL1G29550' => 'aly', 'AL1G37100' => 'aly', 'AL2G18640' => 'aly', 'AL2G29990' => 'aly', 'AL2G32010' => 'aly', 'Aqoxy5G03796' => 'aox', 'Aqoxy7G00931' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5FF9GF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E9MTVL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAU41V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RKV2XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U1CM5Q' => 'arhy', 'AT1G17290' => 'ath', 'AT1G23310' => 'ath', 'AT1G70580' => 'ath', 'AT1G72330' => 'ath', 'ATR0099G036' => 'atr', 'ATR1154G004' => 'atr', 'Atru.chr1.4154' => 'acertr', 'Atru.chr11.2115' => 'acertr', 'Atru.chr11.2131' => 'acertr', 'AUR62001404' => 'cqu', 'AUR62001405' => 'cqu', 'AUR62001407' => 'cqu', 'AUR62005448' => 'cqu', 'AUR62024293' => 'cqu', 'AUR62025615' => 'cqu', 'AUR62025616' => 'cqu', 'AUR62043503' => 'cqu', 'BcaB03g11932' => 'bca', 'BcaB03g13007' => 'bca', 'BcaB03g14823' => 'bca', 'BcaB03g15661' => 'bca', 'BcaB07g32318' => 'bca', 'BcaB07g34034' => 'bca', 'BcaC02g10456' => 'bca', 'BcaC05g25650' => 'bca', 'BcaC05g26240' => 'bca', 'BcaC06g35032' => 'bca', 'BcaC07g38845' => 'bca', 'BcaC07g39193' => 'bca', 'BcaC07g41412' => 'bca', 'BcaC07g41428' => 'bca', 'BcaC08g45714' => 'bca', 'BcaC08g46507' => 'bca', 'BcaC08g47378' => 'bca', 'BcaC08g47379' => 'bca', 'BolC1t03788H' => 'bol', 'BolC5t30275H' => 'bol', 'BolC5t30950H' => 'bol', 'BolC6t38601H' => 'bol', 'BolC6t39521H' => 'bol', 'BolC6t40221H' => 'bol', 'BolC7t42571H' => 'bol', 'BolC7t42963H' => 'bol', 'BolC8t49408H' => 'bol', 'BolC8t49410H' => 'bol', 'BolC8t49413H' => 'bol', 'BolC8t49414H' => 'bol', 'BolC8t49822H' => 'bol', 'BolC8t51945H' => 'bol', 'BraA06t24478Z' => 'bra', 'BraA06t26674Z' => 'bra', 'BraA07t29146Z' => 'bra', 'BraA07t30664Z' => 'bra', 'BraA07t31263Z' => 'bra', 'BraA08t34755Z' => 'bra', 'BraA08t35027Z' => 'bra', 'BraA09t39637Z' => 'bra', 'BraA09t41419Z' => 'bra', 'C01p38260' => 'bna', 'C04p28670' => 'bna', 'C04p51250' => 'bna', 'C05p15690' => 'bna', 'C05p22520' => 'bna', 'C06p35020' => 'bna', 'C06p44570' => 'bna', 'C06p51990' => 'bna', 'C07p20460' => 'bna', 'C08p17820' => 'bna', 'C08p17830' => 'bna', 'C08p21830' => 'bna', 'C08p24200' => 'bna', 'C08p43950' => 'bna', 'CAN.G1821.2' => 'can', 'CAN.G282.55' => 'can', 'CAN.G39.31' => 'can', 'CAN.G665.5' => 'can', 'CAN.G790.59' => 'can', 'CAN.G790.60' => 'can', 'CANSAT01G0937' => 'cansat', 'CANSAT56G0598' => 'cansat', 'CARHR017890' => 'chi', 'CARHR023760' => 'chi', 'CARHR063790' => 'chi', 'CARHR065240' => 'chi', 'CARHR287090' => 'chi', 'Carub.0001s1706' => 'cru', 'Carub.0001s2290' => 'cru', 'Carub.0002s1730' => 'cru', 'Carub.0002s1919' => 'cru', 'Ca_04578_v3' => 'car', 'Ca_23445_v3' => 'car', 'CBR_g3122' => 'cbr', 'CBR_g8420' => 'cbr', 'Cc04_g00710' => 'ccan', 'Cc04_g00730' => 'ccan', 'Cc11_g15580' => 'ccan', 'CDE04G2535' => 'cde', 'CDE05G0136' => 'cde', 'CDE06G0053' => 'cde', 'CDE06G0257' => 'cde', 'CDE06G1663' => 'cde', 'CDE07G0870' => 'cde', 'CDE11G0159' => 'cde', 'Cfa003462' => 'cfa', 'Cfa025431' => 'cfa', 'Ciclev10025334m.g' => 'ccl', 'Ciclev10031381m.g' => 'ccl', 'CiPaw.01G211600' => 'cil', 'CiPaw.02G131100' => 'cil', 'CiPaw.05G183300' => 'cil', 'CiPaw.06G068600' => 'cil', 'ClCG05G025680' => 'cla', 'ClCG07G014290' => 'cla', 'ClCG08G017730' => 'cla', 'ClCG09G001390' => 'cla', 'COL.COLO4_24248' => 'col', 'COL.COLO4_30863' => 'col', 'Cpa.g.sc25.192' => 'cpa', 'Cpa.g.sc33.7' => 'cpa', 'Cre06.g284700' => 'cre', 'Cre10.g451950' => 'cre', 'CsaV3_2G024880' => 'csa', 'CsaV3_3G031010' => 'csa', 'CsaV3_5G031200' => 'csa', 'CsaV3_5G031220' => 'csa', 'CsaV3_7G033940' => 'csa', 'CSS0002139' => 'camsi', 'CSS0014253' => 'camsi', 'CSS0018348' => 'camsi', 'CSS0022394' => 'camsi', 'CSS0040535' => 'camsi', 'CSS0043419' => 'camsi', 'CSS0049060' => 'camsi', 'DCAR_005266' => 'dca', 'DCAR_007059' => 'dca', 'DCAR_010371' => 'dca', 'DCAR_016090' => 'dca', 'DCAR_024439' => 'dca', 'DCAR_026433' => 'dca', 'DCAR_026518' => 'dca', 'DCAR_031149' => 'dca', 'Dinv15240' => 'din', 'Dinv20384' => 'din', 'Dinv24800' => 'din', 'Dinv24801' => 'din', 'Dinv37818' => 'din', 'Duzib192G0338' => 'dzi', 'Duzib192G0538' => 'dzi', 'Duzib235G0453' => 'dzi', 'Duzib251G0743' => 'dzi', 'Duzib268G1209' => 'dzi', 'ECA232G2788' => 'eca', 'ECA233G5725' => 'eca', 'ECA233G5843' => 'eca', 'ECA234G0058' => 'eca', 'ECA234G3109' => 'eca', 'EL10Ac6g13790' => 'bvu', 'EL10Ac7g16494' => 'bvu', 'Eucgr.I02163' => 'egr', 'FAN02G0532' => 'fan', 'FAN05G5808' => 'fan', 'FAN07G1387' => 'fan', 'FAN09G2096' => 'fan', 'FAN12G0602' => 'fan', 'FAN14G3611' => 'fan', 'FAN14G5257' => 'fan', 'FAN17G1512' => 'fan', 'FAN22G0797' => 'fan', 'FvH4_4g25450' => 'fve', 'FvH4_6g35810' => 'fve', 'Glyma.01G026700' => 'gma', 'Glyma.02G038100' => 'gma', 'Glyma.07G045900' => 'gma', 'Glyma.16G013900' => 'gma', 'Gohir.1Z049518' => 'ghi', 'Gohir.A03G136200' => 'ghi', 'Gohir.A10G047500' => 'ghi', 'Gohir.D02G159500' => 'ghi', 'Gohir.D05G143800' => 'ghi', 'Gohir.D10G051700' => 'ghi', 'Gohir.D13G061400' => 'ghi', 'Gohir.D13G129751' => 'ghi', 'Gohir.D13G150201' => 'ghi', 'Gorai.003G054500' => 'gra', 'Gorai.005G179600' => 'gra', 'Gorai.007G155200' => 'gra', 'Gorai.009G147700' => 'gra', 'Gorai.011G055200' => 'gra', 'Gorai.011G073800' => 'gra', 'GSVIVG01004084001' => 'vvi', 'GSVIVG01016669001' => 'vvi', 'HanXRQChr08g0208091' => 'han', 'HanXRQChr09g0277251' => 'han', 'HanXRQChr10g0312021' => 'han', 'HanXRQChr12g0360111' => 'han', 'HanXRQChr16g0498851' => 'han', 'Haze_12238' => 'cav', 'Haze_16134' => 'cav', 'Haze_26979' => 'cav', 'Haze_27292' => 'cav', 'Hma1.2p1_0223F.1_g094110' => 'hma', 'Hma1.2p1_0229F.1_g097080' => 'hma', 'HPP92_010220' => 'vpl', 'HPP92_010225' => 'vpl', 'HPP92_010227' => 'vpl', 'HPP92_017365' => 'vpl', 'Hund05703' => 'sun', 'Hund06022' => 'sun', 'Hund18637' => 'sun', 'Hund25384' => 'sun', 'Lalb_Chr05g0216601' => 'lal', 'Lalb_Chr09g0326161' => 'lal', 'Lalb_Chr09g0326171' => 'lal', 'Lalb_Chr10g0101101' => 'lal', 'Lalb_Chr15g0076701' => 'lal', 'Lalb_Chr16g0381981' => 'lal', 'Lalb_Chr17g0343231' => 'lal', 'Lj2g0008314' => 'lja', 'Lj3g0007506' => 'lja', 'Lj3g0027278' => 'lja', 'Lj5A29T59' => 'lonja', 'Lj6C811T7' => 'lonja', 'Lj9A538T108' => 'lonja', 'Lsat_1_v5_gn_1_86760' => 'lsa', 'Lsat_1_v5_gn_2_58840' => 'lsa', 'Lsat_1_v5_gn_3_27001' => 'lsa', 'Lsat_1_v5_gn_3_50260' => 'lsa', 'Lsat_1_v5_gn_3_64460' => 'lsa', 'Lsat_1_v5_gn_4_182881' => 'lsa', 'Lsat_1_v5_gn_4_92161' => 'lsa', 'Lsat_1_v5_gn_4_92321' => 'lsa', 'Lsat_1_v5_gn_5_137860' => 'lsa', 'Lsat_1_v5_gn_7_61220' => 'lsa', 'Lsat_1_v5_gn_8_150760' => 'lsa', 'Lsat_1_v5_gn_9_23200' => 'lsa', 'Lsat_1_v5_gn_9_50500' => 'lsa', 'Manes.04G150900' => 'mes', 'Manes.11G012700' => 'mes', 'Manes.12G024100' => 'mes', 'Manes.13G025700' => 'mes', 'Mapoly0013s0051' => 'mpo', 'Mapoly0036s0030' => 'mpo', 'Mapoly0041s0090' => 'mpo', 'MBI10_g00739_MAGBIO' => 'mbi', 'MBI13_g01697_MAGBIO' => 'mbi', 'MBI13_g01698_MAGBIO' => 'mbi', 'MBI19_g32872_MAGBIO' => 'mbi', 'MCO11G804' => 'mco', 'MD09G1173000' => 'mdo', 'MD13G1102800' => 'mdo', 'MD16G1103000' => 'mdo', 'MD17G1154300' => 'mdo', 'Medtr5g033230' => 'mtr', 'Medtr8g023140' => 'mtr', 'MELO3C000117.2' => 'cme', 'MELO3C000284.2' => 'cme', 'MELO3C010686.2' => 'cme', 'MELO3C011959.2' => 'cme', 'MELO3C022699.2' => 'cme', 'MELO3C024307.2' => 'cme', 'MELO3C027855.2' => 'cme', 'MELO3C027861.2' => 'cme', 'MELO3C032487.2' => 'cme', 'Migut.D00911' => 'egut', 'Migut.I01131' => 'egut', 'Migut.L01482' => 'egut', 'MSTRG.10911' => 'ama', 'MSTRG.10912' => 'ama', 'MSTRG.7919' => 'ama', 'MSTRG.9542' => 'ama', 'Nitab4.5_0000007g0010' => 'nta', 'Nitab4.5_0000069g0290' => 'nta', 'Nitab4.5_0008337g0070' => 'nta', 'Nitab4.5_0008419g0010' => 'nta', 'Nitab4.5_0010687g0020' => 'nta', 'Nitab4.5_0012219g0010' => 'nta', 'Nitab4.5_0012240g0010' => 'nta', 'Nitab4.5_0012264g0020' => 'nta', 'Nitab4.5_0014572g0010' => 'nta', 'Nn3g16744' => 'nnu', 'Nn4g22644' => 'nnu', 'Nn4g22645' => 'nnu', 'Nn6g35731' => 'nnu', 'Nn8g38516' => 'nnu', 'Oeu001713.1' => 'oeu', 'Oeu001714.1' => 'oeu', 'Oeu019506.1' => 'oeu', 'Oeu019507.1' => 'oeu', 'Oeu028590.1' => 'oeu', 'Oeu038624.2' => 'oeu', 'Oeu059006.3' => 'oeu', 'Os03g0183600' => 'osa', 'Os07g0108300' => 'osa', 'Os07g0617800' => 'osa', 'Os09g0433900' => 'osa', 'Os10g0390500' => 'osa', 'Os10g0390600' => 'osa', 'Peaxi162Scf00021g00192' => 'pax', 'Peaxi162Scf00038g02342' => 'pax', 'Peaxi162Scf00128g00023' => 'pax', 'Peaxi162Scf00207g01543' => 'pax', 'PGR119G0041' => 'pgr', 'PGR119G0977' => 'pgr', 'PGSC0003DMG400004899' => 'stu', 'PGSC0003DMG400016373' => 'stu', 'PGSC0003DMG400018622' => 'stu', 'Phvul.002G150800' => 'pvu', 'Phvul.010G123200' => 'pvu', 'Potri.001G162800' => 'ptr', 'Potri.003G072600' => 'ptr', 'Potri.008G187400' => 'ptr', 'Potri.010G045100' => 'ptr', 'Pp3c10_10600' => 'ppa', 'Pp3c16_6730' => 'ppa', 'Pp3c17_15420' => 'ppa', 'Pp3c25_700' => 'ppa', 'Pp3c2_3470' => 'ppa', 'Pp3c5_10250' => 'ppa', 'PRCOL_00001875' => 'pco', 'PRCOL_00006762' => 'pco', 'PRCOL_00007024' => 'pco', 'Prupe.1G243000' => 'ppe', 'Prupe.3G031100' => 'ppe', 'Psat0s1999g0120' => 'psa', 'Psat0s2922g0080' => 'psa', 'Psat1g170560' => 'psa', 'Psat4g165160' => 'psa', 'PSO104G0211' => 'pso', 'PSO421G0467' => 'pso', 'PSO421G0584' => 'pso', 'PSO541G1077' => 'pso', 'PSO675G9156' => 'pso', 'PSO832G2040' => 'pso', 'QL03p001686' => 'qlo', 'QL03p002184' => 'qlo', 'QL03p058498' => 'qlo', 'QL04p007088' => 'qlo', 'QL05p001253' => 'qlo', 'QL05p013355' => 'qlo', 'QL05p013448' => 'qlo', 'QL11p047969' => 'qlo', 'RcHm_v2.0_Chr2g0147841' => 'rch', 'RcHm_v2.0_Chr4g0432761' => 'rch', 'Rhsim08G0244600' => 'rsi', 'Rhsim12G0112100' => 'rsi', 'Sabra01G0129900' => 'sbr', 'Sabra03G0043400' => 'sbr', 'Sabra10G0023100' => 'sbr', 'SalBow6G2737' => 'sbo', 'SalBow8G5007' => 'sbo', 'Sc01g0005250' => 'sci', 'Sc10g0008010' => 'sci', 'Sc12g0010930' => 'sci', 'Sc14g0008710' => 'sci', 'Sed0003337' => 'sed', 'Sed0006022' => 'sed', 'Sed0012585' => 'sed', 'Sed0021209' => 'sed', 'Sed0021799' => 'sed', 'Sed0023149' => 'sed', 'Sed0023415' => 'sed', 'SEGI_00252' => 'sgi', 'SEGI_13162' => 'sgi', 'SEGI_16703' => 'sgi', 'SEGI_17232' => 'sgi', 'SEGI_18825' => 'sgi', 'SEGI_19261' => 'sgi', 'SEGI_20744' => 'sgi', 'SEGI_21708' => 'sgi', 'SGA_v2.0_scaffold122G33308' => 'sas', 'SGA_v2.0_scaffold228G43270' => 'sas', 'SGA_v2.0_scaffold280G46825' => 'sas', 'SGA_v2.0_scaffold71G23922' => 'sas', 'SGA_v2.0_scaffold8G04190' => 'sas', 'SHI25227' => 'shi', 'SMO117G0231' => 'smo', 'SMO119G0069' => 'smo', 'Solyc01g007940.4' => 'sly', 'Solyc03g123600.4' => 'sly', 'Solyc03g123610.4' => 'sly', 'Solyc05g013380.3' => 'sly', 'Solyc06g063090.4' => 'sly', 'Sopen01g003480' => 'spe', 'Sopen03g041370' => 'spe', 'Sopen03g041380' => 'spe', 'Sopen05g008170' => 'spe', 'Sopen06g022540' => 'spe', 'Sp1g15430' => 'spa', 'Sp1g20750' => 'spa', 'Sp5g25730' => 'spa', 'Sp5g27410' => 'spa', 'Sp5g27420' => 'spa', 'TAR374G1093' => 'tar', 'TAR375G0998' => 'tar', 'TAR383G1029' => 'tar', 'TAR629G3416' => 'tar', 'THA.LOC104812273' => 'tha', 'THA.LOC104822983' => 'tha', 'Thecc.02G257900' => 'tca', 'Thecc.06G130000' => 'tca', 'Thhalv10007290m.g' => 'esa', 'Thhalv10007514m.g' => 'esa', 'Thhalv10018474m.g' => 'esa', 'Thhalv10019459m.g' => 'esa', 'TPR.G38783' => 'tpr', 'TPR.G8711' => 'tpr', 'TWI18G1243' => 'twi', 'TWI23G0193' => 'twi', 'TWI36G0849' => 'twi', 'TWI59G1338' => 'twi', 'TWI79G0738' => 'twi', 'unitig_26.g8914' => 'ugi', 'unitig_749.g13277' => 'ugi', 'unitig_749.g14033' => 'ugi', 'vmacro02725' => 'vma', 'vmacro07671' => 'vma', 'vmacro15087' => 'vma', 'vmacro16208' => 'vma', 'vmacro18767' => 'vma', 'VMungo0331G1042' => 'vmu', 'VMungo1215G3017' => 'vmu', 'Zm00001eb028030' => 'zma', 'Zm00001eb085390' => 'zma', 'Zm00001eb109370' => 'zma', 'Zm00001eb118240' => 'zma', 'Zm00001eb223670' => 'zma', 'Zm00001eb223680' => 'zma', 'Zm00001eb298440' => 'zma', 'Zm00001eb313780' => 'zma', 'Zm00001eb327530' => 'zma', 'Zm00001eb333090' => 'zma' ) $gf_id = 'HOM05D001342' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001342' ) $data_identifier = 'HOM05D001342' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 8, 'bca' => (int) 18, 'bol' => (int) 14, 'bra' => (int) 9, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 1, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 9, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 3, 'lonja' => (int) 3, 'lsa' => (int) 13, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 9, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 8, 'rch' => (int) 2, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 2, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 2, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb333090' $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